An update on my partial RdRp #sarbecovirus tree. This is now the region 15000-16000 with many smaller sequences.
nextstrain.org/community/baba…
Once sample is collected they do a PCR, if positive they sequence the region 15300-15700, if interesting they try to sequence the whole genome
Species: Rhinolophus, 9 Hipposideridae, 2 Human, 2 Civet, 3 Pangolin, 1 Chinese badger, 2 Vesper, 1 Molossidae.
No rhinolophids in America. In other countries rhinolophids were sampled and were negative to CoV or sarbecovirus. Turkey unsampled, there are sarbecoviruses there!
Recently published:
Lebanon, Russia (Sotchi), Croatia, UK.
In the SARS 1&2 clades: the Menglun samples, Thailand,Cambodia, 12 sequences likely from Jinning (where almost all good matches to SARS-CoV come from).
The African lineage was seen only in the great lakes region.
Four clades:
🔹Europe-Africa
🔹SARS2 (Yunnan)
🔹SARS (Yunnan)
🔹HKU3-Rf1 (Hong-Kong,Hubei,Zhejiang,Jilin,Guizhou..)
🔹Unclassified: India, Japan, a small Yunnan lineage.
🔹Outlier: Taiwan, in the Europe-Africa clade (?)
About the spillover potential: overall it is likely low, see all the species sampled in relation to the PREDICT project in a rectangle containing Yunnan and its borders, most (non-Rhinolophus) samples were tested for CoV and didn't contain sarbecoviruses.
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